The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction

Abstract

DNA modification is known to regulate experience-dependent gene expression. However, beyond cytosine methylation and its oxidated derivatives, very little is known about the functional importance of chemical modifications on other nucleobases in the brain. Here we report that in adult mice trained in fear extinction the DNA modification N6-methyl-2’-deoxyadenosine (m6dA) accumulates along promoters and coding sequences in activated prefrontal cortical neurons. The deposition of m6dA is associated with increased genome-wide occupancy of the mammalian m6dA methyltransferase, N6amt1, and this correlates with extinction-induced gene expression. The accumulation of m6dA is associated with transcriptional activation at the brain-derived neurotrophic factor (Bdnf) P4 promoter, which is required for Bdnf exon IV mRNA expression and for the extinction of conditioned fear. These results expand the scope of DNA modifications in the adult brain and highlight changes in m6dA as an epigenetic mechanism associated with activity-induced gene expression and the formation of fear extinction memory.

Depletion of histone methyltransferase KMT9 inhibits lung cancer cell proliferation by inducing non-apoptotic cell death

“…Deciphering the exact pathway by which the knockdown of KMT9α leads to non-apoptotic cell death should be investigated in future studies. Recently, Li et al [35] have correlated N6AMT1 expression with m6dA marks in murine neurons that are associated with activity-induced gene expression. Notably, the experiments by Li et al were performed in post-mitotic neurons suggesting that the functions of KMT9 include but are not limited to regulating proliferation.…”

Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction

“…In this experiment, we used fluorescence-activated cell sorting (FACS) on neurons labeled with the neuronal nuclei marker (NeuN) and activity-regulated cytoskeleton-associated protein (Arc; see Figure 1b ). The NeuN marker allows for differentiation of non-neurons from neurons, and the Arc marker differentiates between recently activated neurons and quiescent neurons 18 . We found that fear extinction-trained mice exhibited significantly higher levels of Adar1 mRNA expression in activated neurons (high Arc) than in quiescent neurons (low in Arc) from the same animal ( Figure 1c ).…”

“…However, Adar1 binding to DNA was minimal during the formation of Z-DNA, suggesting that under these conditions Adar1 does not coordinate the formation of Z-DNA 33 . Instead, DNA methylation 20 – 24 , local salt changes 18 , or endogenous synthesis and release of polyamines 34 may contribute to the formation and stabilization of Z-DNA at these sites. Overall, it may only be through the ability of Z-DNA to modulate downstream events such as gene expression or RNA editing that its functional importance for cellular memory can be observed.…”

“…Because Adar1 is critically involved in RNA editing we next investigated whether ADAR1 binding at DNA repetitive elements also impacts RNA editing of transcripts derived from those loci. We examined all editing sites in RNA expressed in response to fear or fear extinction learning using our previously published FACS-sorted RNA sequencing dataset 18 and examined whether these sites of RNA editing align with annotated SINE/LINEs and Adar1 DNA binding. We discovered a total of 496 genes in which RNA editing had occurred in at least 75% of the high arc samples ( Figure 5a ).…”

Molecularly-Defined Hippocampal Inputs Regulate Population Dynamics in the Prelimbic Cortex to Suppress Context Fear Memory Recall

“…A host of previous work has demonstrated relationships between hippocampal-prefrontal function, BDNF, and fear behavior 15,16 , including work from our laboratory showing that mice with decreased production of activity-dependent BDNF have deficits in fear extinction that co-occur with impaired hippocampal-prefrontal oscillatory synchrony 31 . Transcription from promoter IV of the Bdnf gene in the dorsal hippocampus is correlated with fear memory consolidation 32 and epigenetic modification of promoter IV in the IL is linked with fear extinction 33,34 , findings that suggest that BDNF production from promoter IV may contribute to the mechanism underlying fear behavior 35 . Our lab recently demonstrated that synthetic excitation of cells in the ventral dentate gyrus expressing promoter IV-derived Bdnf transcripts increased freezing during context fear retrieval and concomitantly attenuated vHC-PrL oscillatory synchrony 36 .…”